Canberra called on Wednesday for an Indonesian inquiry into the killing of a Papuan independence leader but could not say whether Australian-trained counter-terrorism police were involved in the death.
Foreign Minister Bob Carr said senior Australian officials had pressed Indonesia on the death in June of Mako Tabuni, a leader in Papua's fight for independence from Jakarta allegedly killed by Indonesia's anti-extremist squad.
Tabuni's supporters told Australian media he was gunned down by plain-clothes officers from Detachment 88, a counter-terrorism squad formed after the 2002 Bali bombings and partly trained and resourced by Australia.
Carr said Australian police included human rights training in their work with the Indonesian police but "we don't run the counter-terrorism forces" and there was a limit to Canberra's responsibility for their activities.
He could not confirm whether Detachment 88 had been involved in Tabuni's death but said several top-level representations had been made to Jakarta calling for a "full and open" investigation into the shooting.
"We think the best way of clarifying the situation is for an inquiry," Carr told ABC Television. "We think it would be in the interest of Indonesia in particular and in the interest of their human rights record in the Papuan provinces."
Carr stressed that the calls came "in the context of us consistently recognising Indonesian sovereignty over Papua, and at the same time asserting our right as a friend and a neighbour to raise human rights issues".
"Even when they're dealing with people who may have used violent means, who are accused of using violent means, our strong position with Indonesia is that the legal process should be open and that the people accused of these offences should be treated with due process," he said.
Carr said Indonesian President Susilo Bambang Yudhoyono and Foreign Minister Marty Natalegawa had been "very responsive".
Australian police said it only provided funding to the Indonesian forces for specific counter-terrorism initiatives, though it had "gifted" cars, telecoms and computer equipment worth Aus$314,500 (US$325,810) over two years.
"The Australian Federal Police is not aware, nor been informed, that Detachment 88 is specifically targeting independence leaders in Papua and West Papua," it said in a statement.